6WEZ

Crystal Structure of Broadly Neutralizing Antibody 3I14-D93N Mutant Bound to the Influenza A H3 Hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unique structural solution from a V H 3-30 antibody targeting the hemagglutinin stem of influenza A viruses.

Harshbarger, W.D.Deming, D.Lockbaum, G.J.Attatippaholkun, N.Kamkaew, M.Hou, S.Somasundaran, M.Wang, J.P.Finberg, R.W.Zhu, Q.K.Schiffer, C.A.Marasco, W.A.

(2021) Nat Commun 12: 559-559

  • DOI: https://doi.org/10.1038/s41467-020-20879-6
  • Primary Citation of Related Structures:  
    6WEX, 6WEZ, 6WF0, 6WF1

  • PubMed Abstract: 

    Broadly neutralizing antibodies (bnAbs) targeting conserved influenza A virus (IAV) hemagglutinin (HA) epitopes can provide valuable information for accelerating universal vaccine designs. Here, we report structural details for heterosubtypic recognition of HA from circulating and emerging IAVs by the human antibody 3I14. Somatic hypermutations play a critical role in shaping the HCDR3, which alone and uniquely among V H 3-30 derived antibodies, forms contacts with five sub-pockets within the HA-stem hydrophobic groove. 3I14 light-chain interactions are also key for binding HA and contribute a large buried surface area spanning two HA protomers. Comparison of 3I14 to bnAbs from several defined classes provide insights to the bias selection of V H 3-30 antibodies and reveals that 3I14 represents a novel structural solution within the V H 3-30 repertoire. The structures reported here improve our understanding of cross-group heterosubtypic binding activity, providing the basis for advancing immunogen designs aimed at eliciting a broadly protective response to IAV.


  • Organizational Affiliation

    Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin319Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A5P1MU07 (Influenza A virus)
Explore A0A5P1MU07 
Go to UniProtKB:  A0A5P1MU07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P1MU07
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin176Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A2P1E3C0 (Influenza A virus)
Explore A0A2P1E3C0 
Go to UniProtKB:  A0A2P1E3C0
Entity Groups  
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UniProt GroupA0A2P1E3C0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
heavy chainC [auth H]235Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
light chainD [auth L]213Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
H [auth F],
I [auth G]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D],
G [auth E],
J [auth I]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.842α = 90
b = 130.842β = 90
c = 189.344γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI121285
Department of Defense (DOD, United States)United StatesW81XWH-15-1-0317

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Refinement description